6-109313253-C-G

Variant names:

• chr6-109313253-C-G
• rs9487060
• ENST00000368966.10:n.4603-810C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000368966.10(CCDC162P):​n.4603-810C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,090 control chromosomes in the GnomAD database, including 5,906 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (5906 hom., cov: 32)
• Consequence: CCDC162P ENST00000368966.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 1 publications found

Genes affected

CCDC162P (HGNC:21565): (coiled-coil domain containing 162, pseudogene) This gene is the ortholog of the mouse coiled-coil domain containing 162 gene. This locus is transcribed, but is represented as a unitary pseudogene because there are multiple changes in the coding sequence, including multiple changes that result in premature stop codons, relative to the mouse coding sequence. Transcripts from this locus are expected to encode truncated proteins, and may be candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Sep 2018]

ENSG00000293541 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.4571-810C>G		intron_variant	Intron 32 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.4603-810C>G		intron_variant	Intron 32 of 45	6
ENSG00000293541	ENST00000473454.7	n.301+5176C>G		intron_variant	Intron 3 of 11	4
ENSG00000293541	ENST00000506861.1	n.348+3599C>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32393 AN: 151972 Hom.: 5887 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.179

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.213 AC: 32460 AN: 152090 Hom.: 5906 Cov.: 32 AF XY: 0.216 AC XY: 16048 AN XY: 74352

African (AFR) AF: 0.492 AC: 20385 AN: 41442

American (AMR) AF: 0.182 AC: 2780 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1511 AN: 5160

South Asian (SAS) AF: 0.138 AC: 665 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0706 AC: 4800 AN: 68010

Other (OTH) AF: 0.180 AC: 381 AN: 2112

Alfa AF: 0.0452 Hom.: 56

Bravo AF: 0.230

Asia WGS AF: 0.224 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.48
PhyloP100		-0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9487060; hg19: chr6-109634456; COSMIC: COSV64535111;